chr7-36755819-G-A

Variant names:

• chr7-36755819-G-A
• rs11977641
• ENST00000419326.1:n.471G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000419326.1(ENSG00000229424):​n.471G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.021 (72 hom., cov: 20)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000229424 ENST00000419326.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 3 publications found

Genes affected

ENSG00000229424 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229424	ENST00000419326.1	n.471G>A		non_coding_transcript_exon_variant	Exon 2 of 3	4
ENSG00000307889	ENST00000829619.1	n.182-15482C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0211 AC: 1576 AN: 74604 Hom.: 72 Cov.: 20

Gnomad AFR AF: 0.0735

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00698

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00114

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0217

Gnomad NFE AF: 0.000249

Gnomad OTH AF: 0.0181

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 142 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 112

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 0.00 AC: 0 AN: 18

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 98

Other (OTH) AF: 0.00 AC: 0 AN: 8

GnomAD4 genome AF: 0.0212 AC: 1580 AN: 74664 Hom.: 72 Cov.: 20 AF XY: 0.0205 AC XY: 724 AN XY: 35384

African (AFR) AF: 0.0735 AC: 1494 AN: 20334

American (AMR) AF: 0.00698 AC: 52 AN: 7446

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1752

East Asian (EAS) AF: 0.00 AC: 0 AN: 994

South Asian (SAS) AF: 0.00114 AC: 2 AN: 1760

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4648

Middle Eastern (MID) AF: 0.0227 AC: 4 AN: 176

European-Non Finnish (NFE) AF: 0.000249 AC: 9 AN: 36116

Other (OTH) AF: 0.0180 AC: 19 AN: 1056

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.65
PhyloP100		0.096

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11977641; hg19: chr7-36795424;